Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
The flag -autorecon2-noaseg seems to no longer be used in version 5.1. i.e. ERROR: Flag -autorecon2-noaseg unrecognized. For edits made to aseg.mgz, could you please let me know what recon-all flags are recommended for version 5.1 for the case described in the email below? Thanks. On Sun, 16 Sep 2012 16:07:20 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote Yes On Sep 16, 2012, at 6:13 PM, Darren Gitelman lt;d-gitel...@northwestern.edugt; wrote: Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit lt;subjidgt; brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg On Sep 16, 2012, at 5:19 PM, Darren Gitelman lt;d-gitel...@northwestern.edugt; wrote: Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFileamp;do=getamp;target=TopoafterBM.jpg I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 lt;3809-error.pnggt; ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg On Sep 16, 2012, at 5:19 PM, Darren Gitelman d-gitel...@northwestern.edu wrote: Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFiledo=gettarget=TopoafterBM.jpg I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 3809-error.png ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit subjid brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg On Sep 16, 2012, at 5:19 PM, Darren Gitelman d-gitel...@northwestern.edu wrote: Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFiledo=gettarget=TopoafterBM.jpg I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 3809-error.png ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: white matter and pial surface don't track sulcus
Yes On Sep 16, 2012, at 6:13 PM, Darren Gitelman d-gitel...@northwestern.edu wrote: Yes. That's it. I tried editing the wm.mgz earlier and deleting all voxels labels as ventricle (250) but that didn't solve the problem. Do I edit the aseg.mgz file and just label it as none in this region? Would I use the command tkmedit subjid brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt When done do I run recon-all -autorecon2-noaseg -autorecon3? Thanks, Darren On Sun, Sep 16, 2012 at 4:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Check the aseg and see if it was labeled ventricle (and make sure it really isn't). You may need to edit the aseg On Sep 16, 2012, at 5:19 PM, Darren Gitelman d-gitel...@northwestern.edu wrote: Hi I have run into an issue that I'm not sure how to correct. What happens is that in some subjects the surfaces don't seem to properly track sulci coming off the medial part of temporo-occipital cortex. Please see green arrows on the attached image. In fact the tutorial on topological defects shows an image with a similar issue, but fixing it is not discussed. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect?action=AttachFiledo=gettarget=TopoafterBM.jpg I have checked and these are sulci and not the occipital extent of the lateral ventricle. Perhaps it is not a problem, or if it is then how to approach fixing it? Thank you, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 3809-error.png ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
